In intermittent streams, deteriorating water quality during drying influences fish survival but the specific effects of individual variables and their interactions are poorly known. During summer 2002 and 2004, fish were surveyed in isolated pools of two lowland intermittent streams in south-east Australia. Despite a low dissolved oxygen (DO, range = 0.4–6.8 mg L–1) and high dissolved organic carbon (DOC, 16–50 mg L–1) concentrations, assemblage composition and abundance of native fish appeared unaffected. In subsequent laboratory experiments, concentrations of DO and DOC were independently manipulated to identify better the tolerance of these species to extremes in environmental conditions. At low DOC concentrations (20 mg L–1), no significant effects were observed. At high DOC concentrations (50, 70 and 80 mg L–1), an interaction was observed between DOC and DO, with significant reductions in resistance (decreased time to loss of buoyancy). At extreme DOC concentrations (99 mg L–1), the effect of DO appeared to have been overridden by a strong effect from DOC (rapid loss of equilibrium). The thresholds observed suggest these species have a high resistance to ‘blackwater events’ caused by leaching of DOC from terrestrial leaf litter. Our findings are consistent with the observed tolerances of fish occupying habitats, both in Australia and elsewhere in the world, where extreme physicochemical conditions are a regular and predictable occurrence.